QUICK NOTES

Taiwan's Feng Chia University has succeeded in boosting the production of hydrogen from biomass to 15 liters per hour, one of the world's highest biohydrogen production rates, a researcher at the university said Friday. The research team managed to produce hydrogen and carbon dioxide (which can be captured and stored) from the fermentation of different strains of anaerobes in a sugar cane-based liquefied mixture. The highest yield was obtained by the Clostridium bacterium.
Taiwan News - November 14, 2008.

Sunday, December 07, 2008

Researchers at the J. Craig Venter Institute (JCVI) have published a paper describing a significant advance in genome assembly in which the team can now assemble the whole bacterial genome, Mycoplasma genitalium, in one step from 25 fragments of DNA. The humble yeast Saccharomyces cerevisiae proves to be the ideal genetic factory for the process. Lead author Daniel G. Gibson, Ph.D. and his team published their results in the online early edition of the journal Proceedings of the National Academy of Sciences (PNAS).

The publication is another milestone in synthetic biology, a young branch of biotechnology that may one day help solve global problems like climate change, lead to new drugs, and generate hyper-efficient, 'endless' biofuels. Promising as it may be, the field is highly controversial and some civil society organisations demand a broader debate about the risks of synthetic biology (earlier post).

The new publication represents major improvements in the methods that the team developed and described in their January 2008 publication of the first synthesis of a bacterial genome, M. genitalium. That publication outlined how the team synthesized in the laboratory the 582,970 base pair M. genitalium genome using the chemical building blocks of DNA—adenine (A), guanine (G), cytosine (C) and thymine (T) (previous post).

While this was a big advance, it took several years to come to fruition and in the end was a tedious, multi- stage process in which the team had to build the genome a quarter at a time using the bacterium Escherichia coli to clone and produce the DNA segments. During this building process the team found that E. coli had difficulty reproducing the large DNA segments, so they turned to the yeast Saccharomyces cerevisiae. They were then able to finish creating the synthetic bacterial genome using a method called homologous recombination (a process that cells naturally use to repair chromosome damage).

Realizing how robustly yeast performed, the team wondered if it could be used to build the entire M. genitalium genome from multiple, smaller, overlapping segments of DNA. For this study the team used DNA fragments that ranged in size from about 17,000 base pairs to 35,000 base pairs. These relatively short segments were inserted into yeast cells in one step and through the mechanism of homologous recombination were assembled into the synthetic M. genitalium genome. Several experiments were then done to confirm that all 25 pieces of the synthetic DNA had been correctly assembled in the yeast cells, and to show that the experiment could be successfully reproduced.

The JCVI team continues to explore the capacity for DNA assembly in yeast, and the various applications of this particular method. They conjecture that a variety of combinations of DNA molecules and genetic pathways could be manufactured in yeast, in essence turning yeast into a genetic factory for specifically designed and optimized processes. This advance is being used by scientists at the company Synthetic Genomics Inc. in making next generation biofuels and biochemicals more efficiently:energy :: sustainability :: biomass :: bioenergy :: biofuels :: synthetic biology :: genomics :: biotechnology ::

We continue to be amazed by the capacity of yeast to simultaneously take up so many DNA pieces and assemble them into genome-size molecules. This capacity begs to be further explored and extended and will help accelerate progress in applications of synthetic genomics. - Dr Gibson, lead author

Senior author Clyde Hutchison, Ph.D., adds that he is astounded by the team’s progress in assembling large DNA molecules. It remains to be seen how far they can push this yeast assembly platform but the team is hard at work exploring these methods as it works to "boot up" the synthetic chromosome.

The work was funded by the company Synthetic Genomics Inc. (SGI), which, among other things, has been active in studying the potential of synthetic genomics for applications in the biofuel sector (previous post).

Key MilestonesThe JCVI builds on a portfolio of major scientific breakthroughs which gradually built up to the current status - a series of applications that may soon make the creation of artificial organisms possible:

Mid-1990’s: After sequencing the M. genitalium genome, Dr. Venter and colleagues begin work on the minimal genome project. This area of research, trying to understand the minimal genetic components necessary to sustain life, started with M. genitalium because it is a bacterium with the smallest genome known that can be grown in pure culture. This work was published in the journal Science in 1995.

2003: Drs. Venter, Smith and Hutchison (along with JCVI's Cynthia Andrews-Pfannkoch) made the first significant strides in the development of a synthetic genome by assembling the 5,386 base pair genome of bacteriophage ΦX174 (phi X). They did so using short, single strands of synthetically produced, commercially available DNA (known as oligonucleotides) and using an adaptation of polymerase chain reaction (PCR), known as polymerase cycle assembly (PCA), to build the phi X genome. The team produced the synthetic phi X in just 14 days.

2007: JCVI researchers led by Carole Lartigue, Ph.D., announced the results of work published in the journal Science, which outlined the methods and techniques used to change one bacterial species, Mycoplasma capricolum, into another, Mycoplasma mycoides Large Colony (LC), by replacing one organism’s genome with the other one’s genome. Genome transplantation was the first essential enabling step in the field of synthetic genomics as it is a key mechanism by which chemically synthesized chromosomes can be activated into viable living cells.

January 2008: The second successful step in the JCVI teams’ journey to create a cell controlled by synthetic DNA was completed when Gibson et al published in the journal Science, the synthetic M. genitalium genome. The team is still working on experiments to install a fully synthetic bacterial chromosome into a recipient cell and thus “boot up” a synthetic chromosome.

Ethical ConsiderationsSince the beginning of the quest to understand and build a synthetic genome, Dr. Venter and his team have been concerned with the societal issues surrounding the work. In 1995 while the team was doing the research on the minimal genome, the work underwent significant ethical review by a panel of experts at the University of Pennsylvania (Cho et al, Science December 1999:Vol. 286. no. 5447, pp. 2087 – 2090). The bioethical group's independent deliberations, published at the same time as the scientific minimal genome research, resulted in a unanimous decision that there were no strong ethical reasons why the work should not continue as long as the scientists involved continued to engage public discussion.

Dr. Venter and the team at JCVI continue to work with bioethicists, outside policy groups, legislative members and staff, and the public to encourage discussion and understanding about the societal implications of their work and the field of synthetic genomics generally. As such, the JCVI’s policy team, along with the Center for Strategic & International Studies (CSIS), and the Massachusetts Institute of Technology (MIT), were funded by a grant from the Alfred P. Sloan Foundation for a 20-month study that explored the risks and benefits of this emerging technology, as well as possible safeguards to prevent abuse, including bioterrorism. After several workshops and public sessions the group published a report in October 2007 outlining options for the field and its researchers.

This report was criticized by a number of organisations, who demand a far broader debate about the potential benefits and risks of synthetic biology (previous post).

CROP NEWS

Researchers at the Taiwan Forestry Research Institute (TFRI) and North Carolina State University in the U.S. have developed genetically modified Eucalyptus trees that store far more carbon dioxide and contain less lignin. - Biopact Sept. 17, 2007

The International Eucalyptus Genome Consortium's sequencing effort has been taken up as a project under the U.S. Dept. of Energy's Joint Genome Project for the year 2008. - Biopact June 12, 2007

Brazilian state of Acre intends to make cattle ranchers reforest land which they have cleared for grazing. The sustainable forestry policy is based on replanting economic tree crops such as mahogany, acai, Brazil nut and palms - BBCNews Sept. 27, 2006

Cassava has one of the highest rates of CO2 fixation and sucrose synthesis for any C3 plant. With this in mind, researchers from Ohio State University develop transgenic cassava with starch yields up 2.6 times higher than normal plants by increasing the sink strength for carbohydrate in the crop. This means cassava makes for a 'super crop' when it comes to both CO2 fixation and carbohydrate production, i.e. sugars, the feedstock for ethanol - Plant Biotechnology Journal - Volume 4/Issue 4 - July 2006

Synthetic Genomics and the Asiatic Centre for Genome Technology Sdn Bhd (ACGT) have created a multi-year research and development joint venture to sequence and analyze the oil palm genome. In-depth genomic analyses will be followed by subsequent studies that will analyze the oil palm’s root and leaf microbial communities, to identify biomarkers and metabolic pathways that affect the plant's growth and viability. Biopact - July, 2007

Researchers at the International Institute for the Semi-Arid Tropics have developed a sweet sorghum for the production of ethanol. The new variety has a very high sugar content in its root. Average yields in trial fields in the Philippines were between 95 to 125 tons, considerably higher than those of sugarcane - ICRISAT - Feb. 28, 2007

Brazilian authorities have given their fiat for field trials with genetically modified sugar cane plants. The Centro de Tecnologia Canavieira (Cane Technology Center - CTC) will test three genetically modified varieties that are expected to yield 15% more sugar - GMO Compass

Bamboo planting can slow deforestation, scientists from the International Center for Research in Agroforestry in Nairobi, Kenya, say. Bamboo rapidly becoming economically beneficial crop with large potential for energy, bioremediation, and afforestation - Chosun (S.Korea) Aug. 30, 2006

"The beauty of miscanthus is that you only have to sow it once...Because of the way it grows, there is no need for fertilisers or chemicals", an English entrepreneur talks about his experience with Miscanthus as an energy crop - Grantham Today Aug. 8, 2006